Muhammad, I think your question is not so much a freesurfer one but more general. You want to run 40 jobs in the background so terminals won't be needed once they are spawned.
The way to do it is issue commands like this: ( cmds for job1; cmds for job2; ... ; cmds for jobM ) & ( cmds for jobM+1; ... ; cmds for job2M ) & The & places each group of M commands in the background. The M jobs will run one after the other. Once you've issued these commands, you probably can simply exit from your terminal and they will continue to run. For freesurfer, I suggest using -openmp 6 to provide access to multiple cores to each job so they complete faster. With -openmp 6 and 40 cores, I would stick with no more than 10 simultaneously running jobs. Hopefully this is helpful. Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Muhammad Naveed Iqbal Qureshi [mniqure...@hotmail.com] Sent: Tuesday, January 20, 2015 8:28 PM To: Freesurfer maillist; fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 131, Issue 28 Hi Bruce, I tried it for 40 subjects for first time yesterday, but eventually 28 terminals were self killed and only 12 subjects were processed successfully. Can you guide me why did it happen. My machine has 40 CPU cores with 256GB ram. Secondly how can I preprocess the incomplete subjects? Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to > From: freesurfer-requ...@nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 131, Issue 28 > To: freesurfer@nmr.mgh.harvard.edu > Date: Tue, 20 Jan 2015 12:00:02 -0500 > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. regarding license.txt file (Kanel, Prabesh) > 2. Re: regarding license.txt file (zkauf...@nmr.mgh.harvard.edu) > 3. converting .nii to .mgz (Borzello, Mia) > 4. using merge_stats_tables to merge broadman areas for multiple > subjects. (Salil Soman) > 5. Re: converting .nii to .mgz (Bruce Fischl) > 6. Re: converting .nii to .mgz (Borzello, Mia) > 7. recon-all on group (Muhammad Naveed Iqbal Qureshi) > 8. standardized community affiliation vector (Alexander Lebedev) > 9. Re: Viewing QDEC results in tksurfer (Worker, Amanda) > 10. mri_convert crash after updating with tracula add update > 2014/05/26 on Ubuntu 14.04 lts (Knut J Bjuland) > 11. Re: converting .nii to .mgz (Bruce Fischl) > 12. Re: recon-all on group (Bruce Fischl) > 13. Re: Viewing QDEC results in tksurfer (Bruce Fischl) > 14. Re: Viewing QDEC results in tksurfer (Worker, Amanda) > 15. Re: converting .nii to .mgz (Douglas N Greve) > 16. Re: Viewing QDEC results in tksurfer (Douglas N Greve) > 17. Re: Contrast files for a complex ANCOVA (involving multiple > categorical covariates) model (Douglas N Greve) > 18. Re: converting .nii to .mgz (Borzello, Mia) > 19. Re: converting .nii to .mgz (mborze...@partners.org) > 20. Re: converting .nii to .mgz (Azeez Adebimpe) > 21. Re: converting .nii to .mgz (Douglas N Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 19 Jan 2015 21:50:51 +0000 > From: "Kanel, Prabesh" <pk...@my.fsu.edu> > Subject: [Freesurfer] regarding license.txt file > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <dm2pr0501mb1231f24679cff66cc41b9cca8c...@dm2pr0501mb1231.namprd05.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I downloaded the latest version of the freesurfer and tried to install it. > After running the installation, I registered my information in > https://surfer.nmr.mgh.harvard.edu/registration.html > > I received an email after few minutes with an information that I have to > replace a text inside the license.txt file. So, I went back and try to do > that. But I cannot locate the license.txt file. It does contain LICENSE file > but doesn't have an information that I need to replace. > > Later, I went back and download the latest version of freesurfer again > thinking I may have made a mistake at first installation but even the later > installation didn't contain any license.txt file. > > The freesurfer that I download was from > https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#Download > > The detail of the file is below > Linux > > CentOS 6 x86_64 (64b) > > stable v5.3.0 > > 15 May 2013 > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz> > > 4.2G > > > Thank you for you time. > > Regards, > > Prabesh? > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150119/c57d6e65/attachment.html > > ------------------------------ > > Message: 2 > Date: Mon, 19 Jan 2015 22:29:18 -0500 (EST) > From: zkauf...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] regarding license.txt file > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Cc: pk...@my.fsu.edu, "freesurfer@nmr.mgh.harvard.edu" > <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <61901.71.233.148.189.1421724558.squir...@mail.nmr.mgh.harvard.edu> > Content-Type: text/plain;charset=iso-8859-1 > > The freesurfer installation does NOT contain a license file. You must > create it, first by creating a file called license.txt in your > FREESURFER_HOME directory, then copy/paste the contents specified in the > email you recieved into the license.txt file. > > -Zeke > > > > Hi, > > > > I downloaded the latest version of the freesurfer and tried to install it. > > After running the installation, I registered my information in > > https://surfer.nmr.mgh.harvard.edu/registration.html > > > > I received an email after few minutes with an information that I have to > > replace a text inside the license.txt file. So, I went back and try to do > > that. But I cannot locate the license.txt file. It does contain LICENSE > > file but doesn't have an information that I need to replace. > > > > Later, I went back and download the latest version of freesurfer again > > thinking I may have made a mistake at first installation but even the > > later installation didn't contain any license.txt file. > > > > The freesurfer that I download was from > > https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#Download > > > > The detail of the file is below > > Linux > > > > CentOS 6 x86_64 (64b) > > > > stable v5.3.0 > > > > 15 May 2013 > > > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz> > > > > 4.2G > > > > > > Thank you for you time. > > > > Regards, > > > > Prabesh? > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 3 > Date: Tue, 20 Jan 2015 03:33:13 +0000 > From: "Borzello, Mia" <mborze...@partners.org> > Subject: [Freesurfer] converting .nii to .mgz > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <3c08ddf81692754ebe6e3ff65a59634ba0a02...@phsx10mb13.partners.org> > Content-Type: text/plain; charset="us-ascii" > > Hi Freesurfers, > > I'm looking at Freesurfer files from are from years ago trying to look at the > ct.anat file. Unfortunately, i have the nifti file and not the mgz file, so > I'm wondering if there is a way to create it. In trying to find an answer > online, I found this: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html > I tried that but got an error. It may be a syntax error; this was my command > line: recon-all -i > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > MG17_SurferOutput > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > > FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > > RedHat release: CentOS release 6.5 (Final) > > Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 > > NMR Center info (/space/freesurfer exists): > > machine: huygens > > SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects > > PWD: /autofs/space/huygens_001/users/mia/subjects > > ssh huygens > setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects > cd /autofs/space/huygens_001/users/mia/subjects > > > 1) MG17 > 2) recon-all -i > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > MG17_SurferOutput > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > 3) ERROR: Flag > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > unrecognized. > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > MG17_SurferOutput > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 > x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s exited with ERRORS at Mon Jan 19 22:27:18 EST 2015 > > For more details, see the log file > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > Thanks so much, > Mia > > > ------------------------------ > > Message: 4 > Date: Mon, 19 Jan 2015 22:33:06 -0500 > From: Salil Soman <salso...@stanford.edu> > Subject: [Freesurfer] using merge_stats_tables to merge broadman areas > for multiple subjects. > To: free surfer <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CABd6wRVJ48R53qrS4WKD73e0y28fS=rm4u_t2mwix+s+1vd...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, > > Following earlier device from this list, I was able to run the > merge_stats_tables command for a single subject as so: > > merge_stats_tables --inputs $SUBJECTS_DIR/SUBJ_ID1/stats/lh.BA.stats > --all-segs --tablefile test_lh_BA_Stats_volumes.txt --meas volume > > But when I tried to pass a series of subjects: > > merge_stats_tables --inputs $SUBJECTS_DIR/SUBJ_ID1/stats/lh.BA.stats > $SUBJECTS_DIR/SUBJ_ID2/stats/lh.BA.stats --all-segs --tablefile > test_lh_BA_Stats_volumes.txt --meas volume > > I get the error "duplicate row found: BA1, not sure if identical data, > therefore stopping!" > > Is there a way to use merge_stats_tables to combine the broadman area > volumes for multiple subjects into 1 table? > > Thanks! > > -Sal > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150119/f52c1663/attachment.html > > ------------------------------ > > Message: 5 > Date: Mon, 19 Jan 2015 22:38:18 -0500 > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] converting .nii to .mgz > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <9696c997-e45a-41b2-90c6-8ee996bd6...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Mia > If all you want to do is convert try > > mri_convert ct.anat.nii ct.anat.mgz > > Cheers > Bruce > > > > > On Jan 19, 2015, at 10:33 PM, Borzello, Mia <mborze...@partners.org> wrote: > > > > Hi Freesurfers, > > > > I'm looking at Freesurfer files from are from years ago trying to look at > > the ct.anat file. Unfortunately, i have the nifti file and not the mgz > > file, so I'm wondering if there is a way to create it. In trying to find an > > answer online, I found this: > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html > > I tried that but got an error. It may be a syntax error; this was my > > command line: recon-all -i > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > MG17_SurferOutput > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > > > > > FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 > > > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > > > > RedHat release: CentOS release 6.5 (Final) > > > > Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 > > > > NMR Center info (/space/freesurfer exists): > > > > machine: huygens > > > > SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects > > > > PWD: /autofs/space/huygens_001/users/mia/subjects > > > > ssh huygens > > setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects > > cd /autofs/space/huygens_001/users/mia/subjects > > > > > > 1) MG17 > > 2) recon-all -i > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > MG17_SurferOutput > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > 3) ERROR: Flag > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > unrecognized. > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > MG17_SurferOutput > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC > > 2014 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s exited with ERRORS at Mon Jan 19 22:27:18 EST 2015 > > > > For more details, see the log file > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > Thanks so much, > > Mia > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > ------------------------------ > > Message: 6 > Date: Tue, 20 Jan 2015 04:30:12 +0000 > From: "Borzello, Mia" <mborze...@partners.org> > Subject: Re: [Freesurfer] converting .nii to .mgz > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <3c08ddf81692754ebe6e3ff65a59634ba0a02...@phsx10mb13.partners.org> > Content-Type: text/plain; charset="us-ascii" > > Hi Bruce, > > Thanks for getting back to me so quickly! > I just tried that and got the following error: > reading from ct.anat.nii... > niiRead(): error opening file > /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii > > I'm wondering if the nifti file is possibly corrupted. Is there a way to > check this? > > Thanks so much, > Mia > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, January 19, 2015 10:38 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] converting .nii to .mgz > > Hi Mia > If all you want to do is convert try > > mri_convert ct.anat.nii ct.anat.mgz > > Cheers > Bruce > > > > > On Jan 19, 2015, at 10:33 PM, Borzello, Mia <mborze...@partners.org> wrote: > > > > Hi Freesurfers, > > > > I'm looking at Freesurfer files from are from years ago trying to look at > > the ct.anat file. Unfortunately, i have the nifti file and not the mgz > > file, so I'm wondering if there is a way to create it. In trying to find an > > answer online, I found this: > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html > > I tried that but got an error. It may be a syntax error; this was my > > command line: recon-all -i > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > MG17_SurferOutput > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > > > > > FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 > > > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > > > > RedHat release: CentOS release 6.5 (Final) > > > > Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 > > > > NMR Center info (/space/freesurfer exists): > > > > machine: huygens > > > > SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects > > > > PWD: /autofs/space/huygens_001/users/mia/subjects > > > > ssh huygens > > setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects > > cd /autofs/space/huygens_001/users/mia/subjects > > > > > > 1) MG17 > > 2) recon-all -i > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > MG17_SurferOutput > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > 3) ERROR: Flag > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > unrecognized. > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > MG17_SurferOutput > > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC > > 2014 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s exited with ERRORS at Mon Jan 19 22:27:18 EST 2015 > > > > For more details, see the log file > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > Thanks so much, > > Mia > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 7 > Date: Tue, 20 Jan 2015 15:15:49 +0900 > From: Muhammad Naveed Iqbal Qureshi <mniqure...@hotmail.com> > Subject: [Freesurfer] recon-all on group > To: Freesurfer maillist <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <blu174-w2495b05a98efdd96261d20c4...@phx.gbl> > Content-Type: text/plain; charset="ks_c_5601-1987" > > Can we apply recon-all on a group of subjects simultaneously? > My system has good enough processing power to preprocess 40 subjects at a > time, but I have to open 40 terminal windows for doing it now. > I need an efficient way to do it. > > Any suggestions? > > > > Best Regards, > > Muhammad > Naveed Iqbal Qureshi > > P please don't print this e-mail unless > you really need to > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150120/f15c2c6b/attachment.html > > ------------------------------ > > Message: 8 > Date: Tue, 20 Jan 2015 11:01:41 +0100 > From: Alexander Lebedev <alexander.vl.lebe...@gmail.com> > Subject: [Freesurfer] standardized community affiliation vector > To: s...@jiscmail.ac.uk, freesurfer@nmr.mgh.harvard.edu > Message-ID: > <caesnhehkrupx3ymzvsamslyc94hdkavuy0w+wffg4ggm5dd...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > *Dear Colleagues,* > > I am sorry if my question is a bit out-of-topic... > I wonder if there is a an opportunity to find a community affiliation > vector estimated using any of the large-scale datasets (like the Human > Connectome Project, for example).. I was just thinking that having > independently estimated community structure (assuming the same age group) > for further extraction of modularity-based metrics makes more sense than > using the exact same sets to estimate both community structure and related > measures like participation and diversity coefficients. > > Thanks in advance! > *===* > *Best Wishes,* > *Alex* > > -- > Alexander V. Lebedev MD PhD | Postdoctoral Researcher > > Department of Neurobiology, Care Sciences and Society | Karolinska > Institutet > > Aging Research Center | 113 30 Stockholm, Sweden | G?vlegatan 16 > > > Center for Age-Related Medicine | Researcher > > Stavanger University Hospital > > 4011 Stavanger, Norway | Armauer Hansens vei 20 > > > Mobile (Sweden): +46 7 659 04 649 > > Skype ID: alexander.vl.lebedev > > alexander.vl.lebe...@gmail.com | www.ki-su-arc.se > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150120/f490bcbb/attachment.html > > ------------------------------ > > Message: 9 > Date: Tue, 20 Jan 2015 12:09:27 +0000 > From: "Worker, Amanda" <amanda.wor...@kcl.ac.uk> > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1421755744074.67...@kcl.ac.uk> > Content-Type: text/plain; charset="iso-8859-1" > > My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh inflate" > d- which is when I got the error. > > I have now tried loading fsaverage first with "tksurfer fsaverage lh > inflated" and it seems to be working fine. > > The problem now is changing the colour scale to display only positive values. > I have played around with the Min, Max and Slope and can't seem to remove > values below zero. What I'm after is a scale showing thickness in mm ranging > from something like 1mm-3.5mm (or if it's easier whatever the min and max > thickness' are for the group) > > Best wishes, > > Amanda > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > Sent: 16 January 2015 19:52 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > what is your command line? > > On 01/16/2015 11:02 AM, Worker, Amanda wrote: > > Hi Doug, > > > > I have set up and run the usual Group Analysis through the command line. I > > have then run " mri_concat output-of-preproc.mgh --mean --o > > mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects > > included in the preprocessing. > > > > I'm now having a problem with visualising this with tksurfer, getting > > ERROR: could not read header info from T1 or orig in > > /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri > > > > Presumably this is because all of the T1/orig are stored in each subjects > > data file and I'm not trying to look at a specific subject. Is there a way > > to get around this problem? > > > > Best wishes, > > > > Amanda > > > > ________________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > > <gr...@nmr.mgh.harvard.edu> > > Sent: 15 January 2015 16:56 > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > > > QDEC will not produce mean maps for each group. If this is something you > > want to do, you will need to do it in the command-line group analysis > > stream. See > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > > > > > > > > > On 01/15/2015 05:25 AM, Worker, Amanda wrote: > >> Hi, > >> > >> I am currently only able to open a thickness map for a single subject > >> using "tksurfer SUBJECT lh inflated". I can use the analysis figures from > >> qdec, but I'd really like to plot the mean thickness for a particular > >> group to compare to others visually. Is this possible? > >> > >> Thanks, > >> > >> Amanda > >> > >> ________________________________________ > >> From: freesurfer-boun...@nmr.mgh.harvard.edu > >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > >> <gr...@nmr.mgh.harvard.edu> > >> Sent: 14 January 2015 23:46 > >> To: freesurfer@nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > >> > >> what is your tksurfer command line? > >> > >> On 01/13/2015 07:12 AM, Worker, Amanda wrote: > >>> Hi, > >>> > >>> > >>> Is it possible to view the results of a qdec analysis (correlation > >>> with a single continuous group) in tksurfer? I am currently unable to > >>> open it and I'm getting an error saying "could not open > >>> file */mri/transforms/talairach.xfm ..no such file or directory" . Is > >>> this a file that is not created with qdec? > >>> > >>> > >>> I'm also trying to visualise group mean thickness' in different > >>> colours to allow difference between groups, that are not significant > >>> in the analysis to be visualised. I cannot find any advice on how to > >>> do this, is this something it's possible to do using either freeview > >>> of tksurfer? > >>> > >>> > >>> Thanks, > >>> > >>> > >>> Amanda > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...@nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended only for the person to whom it > >> is > >> addressed. If you believe this e-mail was sent to you in error and the > >> e-mail > >> contains patient information, please contact the Partners Compliance > >> HelpLine at > >> http://www.partners.org/complianceline . If the e-mail was sent to you in > >> error > >> but does not contain patient information, please contact the sender and > >> properly > >> dispose of the e-mail. > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 10 > Date: Tue, 20 Jan 2015 13:28:04 +0100 > From: Knut J Bjuland <knutjor...@outlook.com> > Subject: [Freesurfer] mri_convert crash after updating with tracula > add update 2014/05/26 on Ubuntu 14.04 lts > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <dub125-w21c6e571647aff983f536c3...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Freesurfer experts,After I added the Tracula update at > http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula, I have been unable to use > mri_onvert. Since I have Ubuntu 14.04, I used the Centos 6 x86_64 version > found at this link. However, when I tried to use mri_convert it segement > fault. I have added the output when I try to convert a dicom to mgz. I am > abel to get this segment fault reproducible. > > > > mri_convert_crash 1/2/1.dcm 001.mgzmri_convert_crash 1/2/1.dcm 001.mgz $Id: > mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $reading from > 1/2/1.dcm...crypt_gkey = (null)Segmentation fault (core dumped) > I was able to get mri_conver to work by use the old version which was > included in Freesurfer 5.3. > mri_convert 1/2/1.dcm 001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 mreuter Exp $reading from 1/2/1.dcm...Getting Series No Scanning > Directory INFO: Found 162 files in 1/2INFO: Scanning for Series Number 2INFO: > found 160 files in seriesINFO: loading series header info. > worked with the same command line. > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150120/e7f051b2/attachment.html > > ------------------------------ > > Message: 11 > Date: Tue, 20 Jan 2015 07:43:04 -0500 (EST) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] converting .nii to .mgz > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.11.1501200742460.5...@gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Mia > > can you please send us the full command line? And also do an ls -l of > that file and include it? > > thanks > Bruce > On Tue, 20 Jan 2015, Borzello, Mia wrote: > > > Hi Bruce, > > > > Thanks for getting back to me so quickly! > > I just tried that and got the following error: > > reading from ct.anat.nii... > > niiRead(): error opening file > > /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii > > > > I'm wondering if the nifti file is possibly corrupted. Is there a way to > > check this? > > > > Thanks so much, > > Mia > > ________________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > > [fis...@nmr.mgh.harvard.edu] > > Sent: Monday, January 19, 2015 10:38 PM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] converting .nii to .mgz > > > > Hi Mia > > If all you want to do is convert try > > > > mri_convert ct.anat.nii ct.anat.mgz > > > > Cheers > > Bruce > > > > > > > >> On Jan 19, 2015, at 10:33 PM, Borzello, Mia <mborze...@partners.org> wrote: > >> > >> Hi Freesurfers, > >> > >> I'm looking at Freesurfer files from are from years ago trying to look at > >> the ct.anat file. Unfortunately, i have the nifti file and not the mgz > >> file, so I'm wondering if there is a way to create it. In trying to find > >> an answer online, I found this: > >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html > >> I tried that but got an error. It may be a syntax error; this was my > >> command line: recon-all -i > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> MG17_SurferOutput > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > >> > >> > >> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 > >> > >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > >> > >> RedHat release: CentOS release 6.5 (Final) > >> > >> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 > >> > >> NMR Center info (/space/freesurfer exists): > >> > >> machine: huygens > >> > >> SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects > >> > >> PWD: /autofs/space/huygens_001/users/mia/subjects > >> > >> ssh huygens > >> setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects > >> cd /autofs/space/huygens_001/users/mia/subjects > >> > >> > >> 1) MG17 > >> 2) recon-all -i > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> MG17_SurferOutput > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > >> 3) ERROR: Flag > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> unrecognized. > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> MG17_SurferOutput > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > >> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC > >> 2014 x86_64 x86_64 x86_64 GNU/Linux > >> > >> recon-all -s exited with ERRORS at Mon Jan 19 22:27:18 EST 2015 > >> > >> For more details, see the log file > >> To report a problem, see > >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > >> > >> Thanks so much, > >> Mia > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > ------------------------------ > > Message: 12 > Date: Tue, 20 Jan 2015 07:46:29 -0500 (EST) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] recon-all on group > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.11.1501200745530.5...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-15" > > Hi Muhammad > > can you really run 40 subjects at the same time? Usually that means you > have a processor farm and it has some mechanism for submitting jobs and > load balancing and such (like qsub). > > cheers > Bruce > On Tue, 20 Jan 2015, Muhammad Naveed > Iqbal Qureshi wrote: > > > Can we apply recon-all on a group of subjects simultaneously? > > My system?has good enough processing power to preprocess 40 subjects at > > a?time, but?I have to open 40 terminal windows?for doing it now. > > I need an efficient way to do it. > > ? > > Any suggestions??? > > > > > > Best Regards, > > Muhammad Naveed Iqbal Qureshi > > P please don't print this e-mail unless you really need to > > > > ? > > > > > > ------------------------------ > > Message: 13 > Date: Tue, 20 Jan 2015 07:47:22 -0500 (EST) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.11.1501200747100.5...@gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Amanda, > click the "truncate" button. > > cheers > Bruce > On Tue, 20 Jan 2015, Worker, Amanda wrote: > > > My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh > > inflate" d- which is when I got the error. > > > > I have now tried loading fsaverage first with "tksurfer fsaverage lh > > inflated" and it seems to be working fine. > > > > The problem now is changing the colour scale to display only positive > > values. I have played around with the Min, Max and Slope and can't seem to > > remove values below zero. What I'm after is a scale showing thickness in mm > > ranging from something like 1mm-3.5mm (or if it's easier whatever the min > > and max thickness' are for the group) > > > > Best wishes, > > > > Amanda > > > > ________________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > > <gr...@nmr.mgh.harvard.edu> > > Sent: 16 January 2015 19:52 > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > > > what is your command line? > > > > On 01/16/2015 11:02 AM, Worker, Amanda wrote: > >> Hi Doug, > >> > >> I have set up and run the usual Group Analysis through the command line. I > >> have then run " mri_concat output-of-preproc.mgh --mean --o > >> mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects > >> included in the preprocessing. > >> > >> I'm now having a problem with visualising this with tksurfer, getting > >> ERROR: could not read header info from T1 or orig in > >> /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri > >> > >> Presumably this is because all of the T1/orig are stored in each subjects > >> data file and I'm not trying to look at a specific subject. Is there a way > >> to get around this problem? > >> > >> Best wishes, > >> > >> Amanda > >> > >> ________________________________________ > >> From: freesurfer-boun...@nmr.mgh.harvard.edu > >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > >> <gr...@nmr.mgh.harvard.edu> > >> Sent: 15 January 2015 16:56 > >> To: freesurfer@nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > >> > >> QDEC will not produce mean maps for each group. If this is something you > >> want to do, you will need to do it in the command-line group analysis > >> stream. See > >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > >> > >> > >> > >> > >> On 01/15/2015 05:25 AM, Worker, Amanda wrote: > >>> Hi, > >>> > >>> I am currently only able to open a thickness map for a single subject > >>> using "tksurfer SUBJECT lh inflated". I can use the analysis figures from > >>> qdec, but I'd really like to plot the mean thickness for a particular > >>> group to compare to others visually. Is this possible? > >>> > >>> Thanks, > >>> > >>> Amanda > >>> > >>> ________________________________________ > >>> From: freesurfer-boun...@nmr.mgh.harvard.edu > >>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > >>> <gr...@nmr.mgh.harvard.edu> > >>> Sent: 14 January 2015 23:46 > >>> To: freesurfer@nmr.mgh.harvard.edu > >>> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > >>> > >>> what is your tksurfer command line? > >>> > >>> On 01/13/2015 07:12 AM, Worker, Amanda wrote: > >>>> Hi, > >>>> > >>>> > >>>> Is it possible to view the results of a qdec analysis (correlation > >>>> with a single continuous group) in tksurfer? I am currently unable to > >>>> open it and I'm getting an error saying "could not open > >>>> file */mri/transforms/talairach.xfm ..no such file or directory" . Is > >>>> this a file that is not created with qdec? > >>>> > >>>> > >>>> I'm also trying to visualise group mean thickness' in different > >>>> colours to allow difference between groups, that are not significant > >>>> in the analysis to be visualised. I cannot find any advice on how to > >>>> do this, is this something it's possible to do using either freeview > >>>> of tksurfer? > >>>> > >>>> > >>>> Thanks, > >>>> > >>>> > >>>> Amanda > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> -- > >>> Douglas N. Greve, Ph.D. > >>> MGH-NMR Center > >>> gr...@nmr.mgh.harvard.edu > >>> Phone Number: 617-724-2358 > >>> Fax: 617-726-7422 > >>> > >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> The information in this e-mail is intended only for the person to whom it > >>> is > >>> addressed. If you believe this e-mail was sent to you in error and the > >>> e-mail > >>> contains patient information, please contact the Partners Compliance > >>> HelpLine at > >>> http://www.partners.org/complianceline . If the e-mail was sent to you in > >>> error > >>> but does not contain patient information, please contact the sender and > >>> properly > >>> dispose of the e-mail. > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...@nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > ------------------------------ > > Message: 14 > Date: Tue, 20 Jan 2015 13:48:46 +0000 > From: "Worker, Amanda" <amanda.wor...@kcl.ac.uk> > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1421761702748.47...@kcl.ac.uk> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Bruce, > > Thanks for your help. Is there a way that I can now change the colour bar, > it's currently red to yellow meaning pretty much the whole brain is red. I'd > like several different colours to illustrate different thickness'. > > I don't seem to be able to edit Mid or Slope. > > Thanks, > > Amanda > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > Sent: 20 January 2015 12:47 > To: Freesurfer support list > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > Hi Amanda, > click the "truncate" button. > > cheers > Bruce > On Tue, 20 Jan 2015, Worker, Amanda wrote: > > > My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh > > inflate" d- which is when I got the error. > > > > I have now tried loading fsaverage first with "tksurfer fsaverage lh > > inflated" and it seems to be working fine. > > > > The problem now is changing the colour scale to display only positive > > values. I have played around with the Min, Max and Slope and can't seem to > > remove values below zero. What I'm after is a scale showing thickness in mm > > ranging from something like 1mm-3.5mm (or if it's easier whatever the min > > and max thickness' are for the group) > > > > Best wishes, > > > > Amanda > > > > ________________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > > <gr...@nmr.mgh.harvard.edu> > > Sent: 16 January 2015 19:52 > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > > > what is your command line? > > > > On 01/16/2015 11:02 AM, Worker, Amanda wrote: > >> Hi Doug, > >> > >> I have set up and run the usual Group Analysis through the command line. I > >> have then run " mri_concat output-of-preproc.mgh --mean --o > >> mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects > >> included in the preprocessing. > >> > >> I'm now having a problem with visualising this with tksurfer, getting > >> ERROR: could not read header info from T1 or orig in > >> /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri > >> > >> Presumably this is because all of the T1/orig are stored in each subjects > >> data file and I'm not trying to look at a specific subject. Is there a way > >> to get around this problem? > >> > >> Best wishes, > >> > >> Amanda > >> > >> ________________________________________ > >> From: freesurfer-boun...@nmr.mgh.harvard.edu > >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > >> <gr...@nmr.mgh.harvard.edu> > >> Sent: 15 January 2015 16:56 > >> To: freesurfer@nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > >> > >> QDEC will not produce mean maps for each group. If this is something you > >> want to do, you will need to do it in the command-line group analysis > >> stream. See > >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > >> > >> > >> > >> > >> On 01/15/2015 05:25 AM, Worker, Amanda wrote: > >>> Hi, > >>> > >>> I am currently only able to open a thickness map for a single subject > >>> using "tksurfer SUBJECT lh inflated". I can use the analysis figures from > >>> qdec, but I'd really like to plot the mean thickness for a particular > >>> group to compare to others visually. Is this possible? > >>> > >>> Thanks, > >>> > >>> Amanda > >>> > >>> ________________________________________ > >>> From: freesurfer-boun...@nmr.mgh.harvard.edu > >>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > >>> <gr...@nmr.mgh.harvard.edu> > >>> Sent: 14 January 2015 23:46 > >>> To: freesurfer@nmr.mgh.harvard.edu > >>> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > >>> > >>> what is your tksurfer command line? > >>> > >>> On 01/13/2015 07:12 AM, Worker, Amanda wrote: > >>>> Hi, > >>>> > >>>> > >>>> Is it possible to view the results of a qdec analysis (correlation > >>>> with a single continuous group) in tksurfer? I am currently unable to > >>>> open it and I'm getting an error saying "could not open > >>>> file */mri/transforms/talairach.xfm ..no such file or directory" . Is > >>>> this a file that is not created with qdec? > >>>> > >>>> > >>>> I'm also trying to visualise group mean thickness' in different > >>>> colours to allow difference between groups, that are not significant > >>>> in the analysis to be visualised. I cannot find any advice on how to > >>>> do this, is this something it's possible to do using either freeview > >>>> of tksurfer? > >>>> > >>>> > >>>> Thanks, > >>>> > >>>> > >>>> Amanda > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> -- > >>> Douglas N. Greve, Ph.D. > >>> MGH-NMR Center > >>> gr...@nmr.mgh.harvard.edu > >>> Phone Number: 617-724-2358 > >>> Fax: 617-726-7422 > >>> > >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> The information in this e-mail is intended only for the person to whom it > >>> is > >>> addressed. If you believe this e-mail was sent to you in error and the > >>> e-mail > >>> contains patient information, please contact the Partners Compliance > >>> HelpLine at > >>> http://www.partners.org/complianceline . If the e-mail was sent to you in > >>> error > >>> but does not contain patient information, please contact the sender and > >>> properly > >>> dispose of the e-mail. > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...@nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 15 > Date: Tue, 20 Jan 2015 11:09:07 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] converting .nii to .mgz > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <54be7da3.7060...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Does that file exist? > > On 01/19/2015 11:30 PM, Borzello, Mia wrote: > > Hi Bruce, > > > > Thanks for getting back to me so quickly! > > I just tried that and got the following error: > > reading from ct.anat.nii... > > niiRead(): error opening file > > /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii > > > > I'm wondering if the nifti file is possibly corrupted. Is there a way to > > check this? > > > > Thanks so much, > > Mia > > ________________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > > [fis...@nmr.mgh.harvard.edu] > > Sent: Monday, January 19, 2015 10:38 PM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] converting .nii to .mgz > > > > Hi Mia > > If all you want to do is convert try > > > > mri_convert ct.anat.nii ct.anat.mgz > > > > Cheers > > Bruce > > > > > > > >> On Jan 19, 2015, at 10:33 PM, Borzello, Mia <mborze...@partners.org> wrote: > >> > >> Hi Freesurfers, > >> > >> I'm looking at Freesurfer files from are from years ago trying to look at > >> the ct.anat file. Unfortunately, i have the nifti file and not the mgz > >> file, so I'm wondering if there is a way to create it. In trying to find > >> an answer online, I found this: > >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html > >> I tried that but got an error. It may be a syntax error; this was my > >> command line: recon-all -i > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> MG17_SurferOutput > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > >> > >> > >> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 > >> > >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > >> > >> RedHat release: CentOS release 6.5 (Final) > >> > >> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 > >> > >> NMR Center info (/space/freesurfer exists): > >> > >> machine: huygens > >> > >> SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects > >> > >> PWD: /autofs/space/huygens_001/users/mia/subjects > >> > >> ssh huygens > >> setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects > >> cd /autofs/space/huygens_001/users/mia/subjects > >> > >> > >> 1) MG17 > >> 2) recon-all -i > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> MG17_SurferOutput > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > >> 3) ERROR: Flag > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> unrecognized. > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> MG17_SurferOutput > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > >> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC > >> 2014 x86_64 x86_64 x86_64 GNU/Linux > >> > >> recon-all -s exited with ERRORS at Mon Jan 19 22:27:18 EST 2015 > >> > >> For more details, see the log file > >> To report a problem, see > >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > >> > >> Thanks so much, > >> Mia > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 16 > Date: Tue, 20 Jan 2015 11:11:55 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <54be7e4b.7060...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > Use View->Configure->Overlay > > > On 01/20/2015 08:48 AM, Worker, Amanda wrote: > > Hi Bruce, > > > > Thanks for your help. Is there a way that I can now change the colour bar, > > it's currently red to yellow meaning pretty much the whole brain is red. > > I'd like several different colours to illustrate different thickness'. > > > > I don't seem to be able to edit Mid or Slope. > > > > Thanks, > > > > Amanda > > > > ________________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > > <fis...@nmr.mgh.harvard.edu> > > Sent: 20 January 2015 12:47 > > To: Freesurfer support list > > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > > > Hi Amanda, > > click the "truncate" button. > > > > cheers > > Bruce > > On Tue, 20 Jan 2015, Worker, Amanda wrote: > > > >> My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh > >> inflate" d- which is when I got the error. > >> > >> I have now tried loading fsaverage first with "tksurfer fsaverage lh > >> inflated" and it seems to be working fine. > >> > >> The problem now is changing the colour scale to display only positive > >> values. I have played around with the Min, Max and Slope and can't seem to > >> remove values below zero. What I'm after is a scale showing thickness in > >> mm ranging from something like 1mm-3.5mm (or if it's easier whatever the > >> min and max thickness' are for the group) > >> > >> Best wishes, > >> > >> Amanda > >> > >> ________________________________________ > >> From: freesurfer-boun...@nmr.mgh.harvard.edu > >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > >> <gr...@nmr.mgh.harvard.edu> > >> Sent: 16 January 2015 19:52 > >> To: freesurfer@nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > >> > >> what is your command line? > >> > >> On 01/16/2015 11:02 AM, Worker, Amanda wrote: > >>> Hi Doug, > >>> > >>> I have set up and run the usual Group Analysis through the command line. > >>> I have then run " mri_concat output-of-preproc.mgh --mean --o > >>> mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects > >>> included in the preprocessing. > >>> > >>> I'm now having a problem with visualising this with tksurfer, getting > >>> ERROR: could not read header info from T1 or orig in > >>> /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri > >>> > >>> Presumably this is because all of the T1/orig are stored in each subjects > >>> data file and I'm not trying to look at a specific subject. Is there a > >>> way to get around this problem? > >>> > >>> Best wishes, > >>> > >>> Amanda > >>> > >>> ________________________________________ > >>> From: freesurfer-boun...@nmr.mgh.harvard.edu > >>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > >>> <gr...@nmr.mgh.harvard.edu> > >>> Sent: 15 January 2015 16:56 > >>> To: freesurfer@nmr.mgh.harvard.edu > >>> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > >>> > >>> QDEC will not produce mean maps for each group. If this is something you > >>> want to do, you will need to do it in the command-line group analysis > >>> stream. See > >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > >>> > >>> > >>> > >>> > >>> On 01/15/2015 05:25 AM, Worker, Amanda wrote: > >>>> Hi, > >>>> > >>>> I am currently only able to open a thickness map for a single subject > >>>> using "tksurfer SUBJECT lh inflated". I can use the analysis figures > >>>> from qdec, but I'd really like to plot the mean thickness for a > >>>> particular group to compare to others visually. Is this possible? > >>>> > >>>> Thanks, > >>>> > >>>> Amanda > >>>> > >>>> ________________________________________ > >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu > >>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > >>>> <gr...@nmr.mgh.harvard.edu> > >>>> Sent: 14 January 2015 23:46 > >>>> To: freesurfer@nmr.mgh.harvard.edu > >>>> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > >>>> > >>>> what is your tksurfer command line? > >>>> > >>>> On 01/13/2015 07:12 AM, Worker, Amanda wrote: > >>>>> Hi, > >>>>> > >>>>> > >>>>> Is it possible to view the results of a qdec analysis (correlation > >>>>> with a single continuous group) in tksurfer? I am currently unable to > >>>>> open it and I'm getting an error saying "could not open > >>>>> file */mri/transforms/talairach.xfm ..no such file or directory" . Is > >>>>> this a file that is not created with qdec? > >>>>> > >>>>> > >>>>> I'm also trying to visualise group mean thickness' in different > >>>>> colours to allow difference between groups, that are not significant > >>>>> in the analysis to be visualised. I cannot find any advice on how to > >>>>> do this, is this something it's possible to do using either freeview > >>>>> of tksurfer? > >>>>> > >>>>> > >>>>> Thanks, > >>>>> > >>>>> > >>>>> Amanda > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer@nmr.mgh.harvard.edu > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> -- > >>>> Douglas N. Greve, Ph.D. > >>>> MGH-NMR Center > >>>> gr...@nmr.mgh.harvard.edu > >>>> Phone Number: 617-724-2358 > >>>> Fax: 617-726-7422 > >>>> > >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> The information in this e-mail is intended only for the person to whom > >>>> it is > >>>> addressed. If you believe this e-mail was sent to you in error and the > >>>> e-mail > >>>> contains patient information, please contact the Partners Compliance > >>>> HelpLine at > >>>> http://www.partners.org/complianceline . If the e-mail was sent to you > >>>> in error > >>>> but does not contain patient information, please contact the sender and > >>>> properly > >>>> dispose of the e-mail. > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>> -- > >>> Douglas N. Greve, Ph.D. > >>> MGH-NMR Center > >>> gr...@nmr.mgh.harvard.edu > >>> Phone Number: 617-724-2358 > >>> Fax: 617-726-7422 > >>> > >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...@nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 17 > Date: Tue, 20 Jan 2015 11:17:54 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Contrast files for a complex ANCOVA > (involving multiple categorical covariates) model > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <54be7fb2.8030...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > If that is the model you want, then you will have to create your own > design matrix. The FSGD format does not allow for some covariates > (Score) to have interaction terms and others (Age) to not. > > doug > > > On 01/18/2015 04:08 PM, lindsay hanford wrote: > > Dear Freesurfer Community, > > > > I'm running into the issue of how to deal with testing the interaction > > effects of a model with multiple categorical variables. I have tried > > bypassing this issue by running multiple separate FSGD analyses, > > however, I wonder if this is the best mention to do this.... > > > > To put it into statistical terms, I am interested in creating a model > > that looks at group differences (2: HC vs Dx), and its interaction > > with test score (2: High vs Low) while still controlling for nuisance > > variables (sex, age). > > in other words: > > > > Cortical Thickness ~ Group + Group*Score + Score + Sex + Age > > Group*Score = interaction term > > > > I am mostly confused with how to appropriately create a contrast file > > that can show the interaction between Group and Score (two categorical > > variables) and STILL regress out the effects of sex. Is this even > > possible using fsgd? > > > > Thank you in advance! > > > > Lindsay > > > > > > > > -- > > Lindsay Hanford, BSc, PhD Candidate > > McMaster Integrative Neuroscience Discovery & Study| *Department of > > Psychology, Neuroscience & Behaviour * > > McMaster University *|* 1280 Main Street West, PC329 Psychology > > Building *|* Hamilton, ON, L8S 4L8 > > 905 525 9140 x24784***|*lindsay.hanf...@gmail.com > > <mailto:lindsay.hanf...@gmail.com> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 18 > Date: Tue, 20 Jan 2015 16:26:34 +0000 > From: "Borzello, Mia" <mborze...@partners.org> > Subject: Re: [Freesurfer] converting .nii to .mgz > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <3c08ddf81692754ebe6e3ff65a59634ba0a02...@phsx10mb13.partners.org> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > full command line: mri_convert ct.anat.nii ct.anat.mgz > > command line: ls -l > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > -rw-rw-r-- 1 miaborz acqcash 32506208 Jan 19 22:12 > /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > I had to send the ct.anat.nii file separately because it was too large of a > file for this email. > > Thanks, > m > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Tuesday, January 20, 2015 7:43 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] converting .nii to .mgz > > Hi Mia > > can you please send us the full command line? And also do an ls -l of > that file and include it? > > thanks > Bruce > On Tue, 20 Jan 2015, Borzello, Mia wrote: > > > Hi Bruce, > > > > Thanks for getting back to me so quickly! > > I just tried that and got the following error: > > reading from ct.anat.nii... > > niiRead(): error opening file > > /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii > > > > I'm wondering if the nifti file is possibly corrupted. Is there a way to > > check this? > > > > Thanks so much, > > Mia > > ________________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > > [fis...@nmr.mgh.harvard.edu] > > Sent: Monday, January 19, 2015 10:38 PM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] converting .nii to .mgz > > > > Hi Mia > > If all you want to do is convert try > > > > mri_convert ct.anat.nii ct.anat.mgz > > > > Cheers > > Bruce > > > > > > > >> On Jan 19, 2015, at 10:33 PM, Borzello, Mia <mborze...@partners.org> wrote: > >> > >> Hi Freesurfers, > >> > >> I'm looking at Freesurfer files from are from years ago trying to look at > >> the ct.anat file. Unfortunately, i have the nifti file and not the mgz > >> file, so I'm wondering if there is a way to create it. In trying to find > >> an answer online, I found this: > >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html > >> I tried that but got an error. It may be a syntax error; this was my > >> command line: recon-all -i > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> MG17_SurferOutput > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > >> > >> > >> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 > >> > >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > >> > >> RedHat release: CentOS release 6.5 (Final) > >> > >> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 > >> > >> NMR Center info (/space/freesurfer exists): > >> > >> machine: huygens > >> > >> SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects > >> > >> PWD: /autofs/space/huygens_001/users/mia/subjects > >> > >> ssh huygens > >> setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects > >> cd /autofs/space/huygens_001/users/mia/subjects > >> > >> > >> 1) MG17 > >> 2) recon-all -i > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> MG17_SurferOutput > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > >> 3) ERROR: Flag > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> unrecognized. > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > >> MG17_SurferOutput > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > >> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC > >> 2014 x86_64 x86_64 x86_64 GNU/Linux > >> > >> recon-all -s exited with ERRORS at Mon Jan 19 22:27:18 EST 2015 > >> > >> For more details, see the log file > >> To report a problem, see > >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > >> > >> Thanks so much, > >> Mia > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 19 > Date: Tue, 20 Jan 2015 16:26:19 GMT > From: mborze...@partners.org > Subject: Re: [Freesurfer] converting .nii to .mgz > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <nihhnv.mov...@transfer.partners.org> > Content-Type: text/plain; charset="utf-8" > > You have received 1 secure file from mborze...@partners.org. > Use the secure link below to download. > Here is the ct.anat.nii file > > Secure File Downloads: > Available until: 30 January 2015 > > Click link to download: > ct.anat.nii ,31,744.34 KB > https://transfer.partners.org/seos/1000/mpd/ui31012015928325bc47f437adc56d49b2dc7b3b9a > You have received attachment(s) within this email. To download the > attachment(s), please click on the link(s) above. This service is provided by > Partners Research Computing. > > http://rc.partners.org/ > mailto:r...@partners.org > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150120/57521768/attachment.html > > ------------------------------ > > Message: 20 > Date: Tue, 20 Jan 2015 17:30:08 +0100 > From: Azeez Adebimpe <ayobimpe2...@hotmail.com> > Subject: Re: [Freesurfer] converting .nii to .mgz > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <dub122-w198e0ff3ed07b7155715d5cd...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Mia, > try to change the name of the nifti file from ct.ana.nii to ctana.nii. > Azeez > > > Date: Tue, 20 Jan 2015 11:09:07 -0500 > > From: gr...@nmr.mgh.harvard.edu > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] converting .nii to .mgz > > > > Does that file exist? > > > > On 01/19/2015 11:30 PM, Borzello, Mia wrote: > > > Hi Bruce, > > > > > > Thanks for getting back to me so quickly! > > > I just tried that and got the following error: > > > reading from ct.anat.nii... > > > niiRead(): error opening file > > > /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii > > > > > > I'm wondering if the nifti file is possibly corrupted. Is there a way to > > > check this? > > > > > > Thanks so much, > > > Mia > > > ________________________________________ > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > > > [fis...@nmr.mgh.harvard.edu] > > > Sent: Monday, January 19, 2015 10:38 PM > > > To: Freesurfer support list > > > Subject: Re: [Freesurfer] converting .nii to .mgz > > > > > > Hi Mia > > > If all you want to do is convert try > > > > > > mri_convert ct.anat.nii ct.anat.mgz > > > > > > Cheers > > > Bruce > > > > > > > > > > > >> On Jan 19, 2015, at 10:33 PM, Borzello, Mia <mborze...@partners.org> > > >> wrote: > > >> > > >> Hi Freesurfers, > > >> > > >> I'm looking at Freesurfer files from are from years ago trying to look > > >> at the ct.anat file. Unfortunately, i have the nifti file and not the > > >> mgz file, so I'm wondering if there is a way to create it. In trying to > > >> find an answer online, I found this: > > >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html > > >> I tried that but got an error. It may be a syntax error; this was my > > >> command line: recon-all -i > > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > >> MG17_SurferOutput > > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > >> > > >> > > >> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 > > >> > > >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > > >> > > >> RedHat release: CentOS release 6.5 (Final) > > >> > > >> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 > > >> > > >> NMR Center info (/space/freesurfer exists): > > >> > > >> machine: huygens > > >> > > >> SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects > > >> > > >> PWD: /autofs/space/huygens_001/users/mia/subjects > > >> > > >> ssh huygens > > >> setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects > > >> cd /autofs/space/huygens_001/users/mia/subjects > > >> > > >> > > >> 1) MG17 > > >> 2) recon-all -i > > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > >> MG17_SurferOutput > > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > >> 3) ERROR: Flag > > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > >> unrecognized. > > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii > > >> MG17_SurferOutput > > >> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ > > >> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC > > >> 2014 x86_64 x86_64 x86_64 GNU/Linux > > >> > > >> recon-all -s exited with ERRORS at Mon Jan 19 22:27:18 EST 2015 > > >> > > >> For more details, see the log file > > >> To report a problem, see > > >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >> > > >> > > >> Thanks so much, > > >> Mia > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom it is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150120/e72ab494/attachment.html > > ------------------------------ > > Message: 21 > Date: Tue, 20 Jan 2015 11:34:37 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] converting .nii to .mgz > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <54be839d.5050...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > Can you put this on our file drop? > > > On 01/20/2015 11:26 AM, mborze...@partners.org wrote: > > * > > You have received 1 secure file from mborze...@partners.org. > > * > > Use the secure link below to download. > > Here is the ct.anat.nii file > > Secure File Downloads: > > Available until: **30 January 2015** > > Click link to download: > > *ct.anat.nii* > > <https://transfer.partners.org/seos/1000/mpd/ui31012015928325bc47f437adc56d49b2dc7b3b9a> > > 31,744.34 KB > > You have received attachment(s) within this email. To download the > > attachment(s), please click on the link(s) above. This service is > > provided by Partners Research Computing. > > > > http://rc.partners.org/ > > mailto:r...@partners.org > > > > Secured by Accellion <http://www.accellion.com> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 131, Issue 28 > ******************************************* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
